Just what Deutsche Bank needed: another reason for investors to doubt its balance sheet.

The German banking giant has been called out by examiners at the Federal Reserve Bank of New York for reporting unreliable numbers about its US operations since 2002, according to The Wall Street Journal. The regulator voiced concerns about systems and controls at the bank's US arm and even whether its reporting in general is reliable or accurate.

That raises questions about Deutsche Bank's books overall: the US operations reportedly could equal nearly one-quarter of the firm's total balance sheet.

Investor reaction was somewhat muted Wednesday, possibly because many already take a dim view of Deutsche. The stock trades at just half of book value. Apart from its troubled domestic rival, Commerzbank, the only big European banks that trade at lower multiples of price-to-book value are Italy's Banca Monte dei Paschi di Siena and Banco Espírito Santo of Portugal.

In Deutsche's favor, it appears to have time to sort out these issues and has committed to spending an extra €1 billion ($1.35 billion) in systems investment and staff increases to deal with this and other regulatory demands since December, when the New York Fed sent its letter.

That said, internal controls have taken on greater importance with US regulators after problems in this area were said to have played a role in JP Morgan's "London whale" trading debacle.

Furthermore, Deutsche is already undercapitalized in the US by its own estimation and may have riled the Fed by lobbying against its proposals for foreign-bank capital requirements. These were adopted earlier this year.

Deutsche's exact capital position in the US isn't now readily apparent in regulatory filings due to a change in its structure in 2012. But in its last filing as a bank holding company in December 2011, the US operations had total assets of $355 billion and Tier 1 capital of negative $5.68 billion.

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Also, any doubts at the Fed about the bank's asset valuations and controls could lead to demands that it hold more capital or to restrictions that crimp its fixed-income trading business.

Investors were never expecting Deutsche's US businesses to be able to pay dividends up to the group after a scheduled capital review in 2016 because of its low capital base—another potential reason behind the muted share-price reaction Wednesday.

However, any limitations on its fixed-income trading operations in the US would hurt its ambitions to boost profits by becoming the only significant European presence left in this global market—a key pillar of its plan to generate a 12% return on equity by 2016.

The German bank's leadership says the investor skepticism it faces relates mainly to those return targets, as well as some residual fear about the cost of litigation settlements. That may be shortsighted.

This latest embarrassment is actually another reason for shareholders to ascribe a higher cost of equity to the German bank to account for the uncertainty in its businesses as well as the risks. That raises the bar for the return the bank needs to generate to create value.

The bank's leadership can't afford more slips, particularly Anshu Jain, the co-chief executive who previously ran the investment bank and headed its US operations. Deutsche raised €8 billion in equity this year, having pledged last year after a nearly €3 billion capital raise that it wouldn't need to do more.

Deutsche Bank says it now has enough capital for all "known challenges." Its valuation shows, though, that markets don't necessarily buy this line.

Indeed, even after the capital raisings, the bank's leverage ratio at 3.4% remains worryingly low given its heft. Only Crédit Agricole and Societe Generale are worse on this measure in Europe and even adjusting for accounting differences it falls short of most US rivals.

If missteps in the US mean Deutsche Bank must come back to shareholders for more equity, that should lead to changes at the top.